From 422ad3be3a4f30383e41aa96767ca66bdb4013b1 Mon Sep 17 00:00:00 2001
From: ekiernan <ekiernan@broadinstitute.org>
Date: Fri, 10 Jan 2025 20:01:53 -0500
Subject: [PATCH] testing fix for wdl gtf_path syntax

---
 pipelines/skylab/atac/atac.wdl | 3 ++-
 tasks/skylab/H5adUtils.wdl     | 2 +-
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/pipelines/skylab/atac/atac.wdl b/pipelines/skylab/atac/atac.wdl
index 437a87fa5f..92037920b8 100644
--- a/pipelines/skylab/atac/atac.wdl
+++ b/pipelines/skylab/atac/atac.wdl
@@ -521,6 +521,7 @@ task CreateFragmentFile {
     String atac_nhash_id = ""
     String input_id
     Int atac_expected_cells = 3000
+    String gtf_path = annotations_gtf
   }
 
   parameter_meta {
@@ -605,7 +606,7 @@ task CreateFragmentFile {
     # Add GTF to uns field
     
     # Original path from args.annotation_file
-    gtf_path = str(~{annotations_gtf})  # e.g., '/cromwell_root/gcp-public-data--broad-references/hg38/v0/star/v2_7_10a/modified_v43.annotation.gtf'
+    gtf_path = "~{gtf_path}"  # e.g., '/cromwell_root/gcp-public-data--broad-references/hg38/v0/star/v2_7_10a/modified_v43.annotation.gtf'
 
     # # Transform the path
     # if annotation_gtf.startswith('/cromwell_root/'):
diff --git a/tasks/skylab/H5adUtils.wdl b/tasks/skylab/H5adUtils.wdl
index f5bb418e91..8d5b279c56 100644
--- a/tasks/skylab/H5adUtils.wdl
+++ b/tasks/skylab/H5adUtils.wdl
@@ -79,7 +79,7 @@ task OptimusH5adGeneration {
           ~{"--input_name_metadata_field " + input_name_metadata_field} \
           --count_matrix ~{sparse_count_matrix} \
           --expression_data_type "exonic" \
-          --pipeline_version ~{pipeline_version}
+          --pipeline_version ~{pipeline_version} \
           --gtf_path $gtf_path
     else
         python3 /warptools/scripts/create_snrna_optimus_full_h5ad.py \